+Open data
-Basic information
Entry | Database: PDB / ID: 4r68 | ||||||
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Title | Lactate Dehydrogenase in complex with inhibitor compound 31 | ||||||
Components | L-lactate dehydrogenase A chain | ||||||
Keywords | OXIDOREDUCTASE / nicotinamide adenine dinucleaotide | ||||||
Function / homology | Function and homology information oxidoreductase complex / lactate metabolic process / Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion ...oxidoreductase complex / lactate metabolic process / Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / membrane / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.112 Å | ||||||
Authors | Eigenbrot, C. / Ultsch, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2014 Title: Optimization of 5-(2,6-dichlorophenyl)-3-hydroxy-2-mercaptocyclohex-2-enones as potent inhibitors of human lactate dehydrogenase. Authors: Labadie, S. / Dragovich, P.S. / Chen, J. / Fauber, B.P. / Boggs, J. / Corson, L.B. / Ding, C.Z. / Eigenbrot, C. / Ge, H. / Ho, Q. / Lai, K.W. / Ma, S. / Malek, S. / Peterson, D. / Purkey, H. ...Authors: Labadie, S. / Dragovich, P.S. / Chen, J. / Fauber, B.P. / Boggs, J. / Corson, L.B. / Ding, C.Z. / Eigenbrot, C. / Ge, H. / Ho, Q. / Lai, K.W. / Ma, S. / Malek, S. / Peterson, D. / Purkey, H.E. / Robarge, K. / Salphati, L. / Sideris, S. / Ultsch, M. / VanderPorten, E. / Wei, B. / Xu, Q. / Yen, I. / Yue, Q. / Zhang, H. / Zhang, X. / Zhou, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r68.cif.gz | 291.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r68.ent.gz | 235.6 KB | Display | PDB format |
PDBx/mmJSON format | 4r68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/4r68 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/4r68 | HTTPS FTP |
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-Related structure data
Related structure data | 4r69C 4m49S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the crystallographic asymmetric unit contains the biological assembly, a homotetramer |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36603.473 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA, PIG19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00338, L-lactate dehydrogenase |
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-Non-polymers , 5 types, 950 molecules
#2: Chemical | ChemComp-NAI / #3: Chemical | ChemComp-EPE / #4: Chemical | ChemComp-W31 / ( #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG 3350, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→57.124 Å / Num. all: 70298 / Num. obs: 70252 / % possible obs: 96.8 % / Observed criterion σ(F): 1.33 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.5 Å2 / Rsym value: 0.098 / Net I/σ(I): 10.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4M49 Resolution: 2.112→57.124 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 21.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.112→57.124 Å
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Refine LS restraints |
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LS refinement shell |
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